You don't say how long is a "long time," what your current game speed is, or how many villagers you have. If you have more than, oh, 15 villagers or so, it's possible to run out of food before the new crops come in. These are hungry villagers!

Your farmers will want to water the farm whenever there are no crops, although you can make them gather from the berry bush. Most people get to level 3 of Harvesting as soon as possible so that the food source is constant and plentiful.